From b67f62746fd08442a358e81d8c31168554006965 Mon Sep 17 00:00:00 2001
From: tpollina <thibaut.pollina@gmail.com>
Date: Thu, 30 Jan 2020 17:52:00 +0100
Subject: [PATCH] Create StackFlow_v3.py

---
 scripts/StackFlow_v3.py | 116 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 116 insertions(+)
 create mode 100644 scripts/StackFlow_v3.py

diff --git a/scripts/StackFlow_v3.py b/scripts/StackFlow_v3.py
new file mode 100644
index 0000000..82f7110
--- /dev/null
+++ b/scripts/StackFlow_v3.py
@@ -0,0 +1,116 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+################################################################################
+# A) Import the librairies needed to execute the script
+################################################################################
+#Activate pinout to control the LEDs and the RELAY
+from gpiozero import LED
+#Allow to access the I2C BUS from the Raspberry Pi
+import smbus
+#Time librairy in order to sleep when need
+from time import sleep
+#Picamera library to take images
+from picamera import PiCamera
+#Enable calculation of remaining duration and datetime
+from datetime import datetime, timedelta
+#Enable creation of new folders
+import os
+from adafruit_motor import stepper
+from adafruit_motorkit import MotorKit
+from time import sleep
+
+kit = MotorKit()
+pump_stepper = kit.stepper1
+pump_stepper.release()
+
+
+################################################################################
+# C) Configuration file
+################################################################################
+
+
+camera = PiCamera()
+camera.resolution = (3280, 2464)
+camera.iso = 60
+sleep(3)
+camera.shutter_speed = 300
+camera.exposure_mode = 'off'
+g = camera.awb_gains
+camera.awb_mode = 'off'
+camera.awb_gains = g
+nb_frame=2000
+
+pump_stepper.release()
+################################################################################
+# E) Define simple functions making the whole sequence
+###
+
+################################################################################
+
+    
+print("###############") 
+print("IMAGING")
+print("###############")
+
+#Inform on the statut of the operation
+print("Imaging : engaged")
+#start the preview only during the acquisition
+camera.start_preview(fullscreen=False, window = (160, 0, 640, 480))
+
+
+#get the actual date
+date_now = datetime.now().strftime("%m_%d_%Y")
+day_now="/home/pi/Desktop/PlanktonScope_acquisition/"+str(date_now)
+
+#create a directory if the directory doesn't exist yet
+if not os.path.exists(day_now):
+    os.makedirs(day_now)
+    
+#get the actual date
+hour_now = datetime.now().strftime("%H")
+hour="/home/pi/Desktop/PlanktonScope_acquisition/"+str(date_now)+"/"+str(hour_now)
+
+#create a directory if the directory doesn't exist yet
+if not os.path.exists(hour):
+    os.makedirs(hour)
+    
+
+#allow the camera to warm up
+
+for i in range(200):
+    pump_stepper.onestep(direction=stepper.BACKWARD, style=stepper.SINGLE)
+    sleep(0.01)
+    
+for frame in range(nb_frame):
+    
+    #get the time now
+    time = datetime.now().strftime("%M_%S_%f")
+    #create a filename from the date and the time
+    filename="/home/pi/Desktop/PlanktonScope_acquisition/"+str(date_now)+"/"+str(hour_now)+"/"+str(time)+".jpg"
+
+    #capture an image with the specified filename
+    camera.capture(filename)
+    
+    #wait to complete the imaging process and print info on the terminal
+    print("Imaging : "+str(frame)+"/"+str(nb_frame))
+    
+    for i in range(10):
+        pump_stepper.onestep(direction=stepper.BACKWARD, style=stepper.SINGLE)
+        sleep(0.01)
+    sleep(0.5)
+        
+
+#stop the preview during the rest of the sequence
+camera.stop_preview()
+pump_stepper.release()
+
+#Inform on the statut of the operation
+print("Imaging : done")
+
+
+################################################################################
+
+#################################################
+# F) Execute the sequence
+################################################################################